Table 1.

Functions in the RAD package

Function	Demo code
compress_module	B_M = compress_module(B, module)
estimate_number	k = estimate_number(B_M)
estimate_clones	C_M, F = estimate_clones(B_M, k)
estimate_marker	C_P = estimate_marker(B_P, F)
	C = estimate_marker(B, F)

Note: The five-line demo shows a typical application of RAD package, which takes as input the bulk RNA data $\mathbf{B}$, bulk marker data ${\mathbf{B}}_{\mathrm{P}}$ and gene module knowledge, and outputs deconvolved RNA $\mathbf{C}$, biomarker ${\mathbf{C}}_{\mathrm{P}}$, and fractions $\mathbf{F}$.